Mega Man X: The Vile Virus
by Mr. Zombie
Summary: Immediately after the events of Mega Man X3, peace is restored once again. However, X is not himself and he slowly heads towards insanity as a Virus is unleashed into his mind after he defeated his old rival Vile for the last time. Vile fans should like!
1. Prologue

Prologue

With the collapse of the so-called utopia of "Doppler Town" and the defeat of Sigma and his Maverick followers, peace was restored once again. The planet had been damaged, and construction processes begin immediately to repair the hurt planet. Both human and Reploid co-exist once again.

The Sigma Virus was thought to be destroyed, but within weeks of Sigma's defeat, small numbers of Reploids begin to go Maverick with no warning at all. The problem, however, is considered minor as the Maverick Hunters deal with these Mavericks with extreme efficiency. Mega Man X, however, is not himself these days. He is constantly haunted by the faces of those he has killed, and those that have almost killed him. X is driven more and more towards insanity as a Virus unleashed from an old rival enters his mind. This is where it begins. . . . .


	2. Chapter I

**Mega Man X: The Vile Virus**

**Chapter I**

"I will haunt you to the day you die. . ."

Those were the last words spoken by the Maverick Vile. Vile had been more then just a Maverick. He had thought freely and did things his own way. Despite the influence of the Maverick Virus, he had managed to in a way manipulate the Virus into his own personality. Despite his great successes from his violent methods, X had stopped him. His hatred for X went far beyond anything else. The urge for revenge was clearly apparent.

Vile's last words had been a promise, not an empty threat! X believed that after that final encounter he would no longer have to worry about Vile. Little did he know that Vile's death was only the beginning.

The Vile Virus has arrived. The consequences it will have on X will be extreme.

-----

**MAVERICK HUNTER HQ**

Sigma's recent defeat brought a new era of peace to the world. The utopian dream known as Doppler Town had failed, but at least even Dr. Doppler had sacrificed himself for the greater good in the end. There were no longer any readings regarding the Sigma Virus. It had disappeared with Sigma and the rest of the Mavericks. Humans and Reploids could once again co-exist in a world of peace. The world, however, was never at peace. That's why the Maverick Hunters still existed.

X had more then earned a vacation, but there was no vacation in this job. Zero had insisted that X leave for a break, but X had refused. Dr. Cain, the old man responsible for the Reploids and X's awakening, fell asleep early. X volunteered to watch the HQ for the night, but Zero convinced him otherwise. Zero offered to watch the progress of the security bots for the night while X got some rest.

So X went to sleep while Zero watched the monitors. The previous battle was still fresh in X's mind, and he dreamed of it. He first remembered the fight with Sigma. Yet again Sigma had returned to carry out his belief that the world should be cleansed of the human race. This time had been close. With Doppler's help Sigma had returned to physical form, but that wasn't the only one who had been revived.

The "T" shaped helmet suddenly appeared before him. Vile! X's first encounter with Vile was remembered more then his fight with Sigma. X had finally decided to help fight the Mavericks after wondering about his purpose, and Vile had nearly killed him right at the beginning. Zero had even sacrificed himself to kill Vile later on, and even that had failed. Only X had been able to kill Vile, not once but twice. Vile had sought revenge and even destroyed the factory to get him. X feared Vile because Vile did as he pleased without any restraints. To him, killing was a bonus, and he enjoyed it very much.

X didn't know why, but he constantly kept looking back on Vile and remembering his final threat. Even in his mind he could hear Vile's sinister voice clearly: "I'll be back, X! You will see! Ha! Ha! Ha!"

It was the insane laughter of someone who cared for no one. No wonder Sigma had chosen Vile to originally command his Maverick Army. Vile had almost done it, but X had stopped him. Perhaps Vile had been right, he was truly haunting him. But why was X so affected by him? Why did his image keep appearing?

X didn't have a peaceful sleep, and he was suddenly awakened by the alarm. In no time he was out of bed and onto his feet. Something was wrong. The alarm, however, went off instantly. False alarm? He ran to the command control room just in case. Zero was still there, and he sighed when he saw X.

"Don't worry, X! I turned the alarm off myself. There's a little problem going on at a factory a few miles from here, nothing major. I'm sending a few of the Hunters to deal with it."

X was immediately concerned. "A problem? What kind of problem, Zero? The Mavericks are destroyed!"

Zero was calm as always. "Take it easy, X. We both know it will take some time for the Virus to be completely wiped out. This is good training for our Hunters."

But X would have none of that! Any kind of problem that involved Mavericks would be dealt with by him personally. "Recall them, Zero. I'll go by myself and deal with this."

Zero sighed once again. Was he serious? "X, this is an extremely small problem. Sure there are some humans that have been taken hostage, but our guys are getting better at taking out these kinds of Mavericks. This problem is nothing compared to what we're used to, X! How about we let it go and let the troops handle it?"

X shook his head. "Sorry Zero, but I feel I have to investigate this myself! Recall them and brief me on the location when I get to the streets!"

Zero shrugged. "Your call, X. I still think it's a waste of time though."

And with that he ordered the recall orders while X ran out of the room. As he ran through the halls he thought to himself that perhaps he kept having these strange dreams because the Maverick threat wasn't truly destroyed. With the Mavericks completely gone perhaps he could be at peace. . . .

-----

The factory was a small one made mostly of reploid workers with a few human employees that all held supervisor positions. While the reploids worked on the assembly lines, they were given orders from the humans from above. They controlled the workers by way of "Manager Bots," humanoid reploids that were meant to oversee the progress of the factory. The late night shift, however, had became disgruntled with their work and these humans. They saw no use for these people, as all the labor and technical work fell upon them. These were signs of the Maverick Virus. Finally, thanks to the influence the Virus had over the Manager Bot, the six workers on that shift went Maverick quickly and the four human employees working that night were take hostage immediately.

Instead of the small electrical appliances they were supposed to be making, they began to make weapons. The people were all tied up in the corner and the huge Manager Bot paced back in forth in front of the conveyer belt.

"Soon, my brothers, we will bring more Reploids to our cause! We will make weapons for our brothers so that we may arm ourselves for the future war against the humans! Victory will be ours!"

Seven Mavericks. Six of them were small worker bots that carried light weapons. They had a human-like upper body but rolled around on treads.

"These humans won't be killed just yet," the Manager declared. "We will kill them publicly so all our brothers can see!"

In the meantime, X had already infiltrated their small factory and heard everything this Manager Bot had to say. He wanted to waste no time in taking out this threat.


	3. Chapter 2

**Chapter II**

X could see the human workers quite clearly. All four had simply been tied up in a corner and weren't even being supervised. The reploids were now considered Maverick, and they all focused on the construction of their weapons. He wanted to deal with this as quickly as possible to avoid any human fatalities. The Manager continued to ramble on about the "Maverick Revolution" when X leapt out of his hiding place.

The Manager spun around quite surprised. He was actually a foot taller then X, and was no small individual. "How did you find us so quickly?!" he exclaimed surprised. "No matter! You're finished!"

He aimed the gun, but was much too slow. X blasted him with a charged X-Buster shot. The Manager was knocked to the ground, smoke rising from him. Surprisingly, he lived.

"Kill him! He is a traitor to our cause!" the Manager shouted angrily.

The small workers picked up the small blaster pistols they had constructed and opened fire. X was quick, much quicker then any of them. He dashed around the room, dodging the small yellow laser shots with relative ease. X had a semi-charged shot for each of these guys. With each green blast he fired, a worker exploded. It was no challenge whatsoever for X.

In the meantime, the Manager rose to his feet. He was hurt badly, but still able to think and move. Unlike the others, who were armed with very light weapons, his was a slightly bigger rifle-style blaster. He charged it up and aimed at the powerful blue fighter, who was busy destroying his loyalists. With a laugh he fired, but it missed! X had disappeared and avoided it completely.

"What?!" he exclaimed.

X was behind him in no time. "Nice try!" he shouted and fired a charged up shot right in the Manager's back. "Damn you!" he shouted as he was torn in half. The explosion quickly followed, and that was that. The others had been killed. His communications link activated immediately with Zero's voice: "Well done, X. You made short work of them just as I thought. Why must you insist on wasting your time with scum like that?"

Zero made a small laugh at his last remark. "Anyway, you might as well head back. I'll send a cleanup crew to get that place cleared…. At least _they_ will get some practice at their job!"

X couldn't help but to smile. He freed the people, who were most thankful for his help. Then he left in a hurry, not wanting to waste anymore time here. He felt more at ease knowing that he had destroyed another Maverick threat. It was most reassuring.

X returned to a very quiet Maverick Hunter HQ. He walked past the command control room and saw Zero still in there. His feet were up on the control pad and he was leaning back in his chair.

"Welcome back, X," Zero said. "Are you going to get some sleep now?"

X smiled and nodded. "Yeah, I guess I will get some sleep now Zero. Wake me if any problems occur!"

"I'm sure you'll hear the alarm if anything happens, X. See ya!"

X nodded and left. He supposed he might as well get some sleep. In his quarters, which were nothing fancy, he went to sleep quite quickly. Maybe he was tired after all. For some reason, however, as it had been since his last major battle, his mind drifted to the past. Dr. Cain had awakened X. X had decided that it was his purpose to help in the fight against the Mavericks. Then there had been Vile. That Maverick had been the most insidious of them all. He used his Ride Armor very skillfully, and in no time he had made short work of X.

"A worthless piece of scrap metal is all you are, X!" Vile's evil voice shouted at him in what seemed like the distance. "That is all you will ever be!"

But it had continued. Vile had tricked Zero into following him. Not even Zero, whom X thought was the most powerful reploid he had seen at the time, could defeat Vile in his Ride Armor. X had gotten better by then, but not even his new upgrades and abilities could stop Vile in that damn Ride Armor. Zero had sacrificed himself to destroy Vile once and for all.

"What a worthless gesture!" Vile's voice shouted at him. And then his laughter, always with the laughter! X wanted the laughter to stop. Why couldn't he just be at peace?

Despite it all, X had defeated Vile. Zero had gotten rid of the Ride Armor at least, and X had fought him head on. Vile had been strong, like a much more upgraded version of himself. But X had prevailed. _I always prevail_, X thought to himself. _If Sigma or Vile or any of those others return, I'll just take care of them again and again! I'll always be there to stop them!_

In a way this reassured him, and while he slept he heard nothing more of Vile's voice the rest of the night.

The morning seemed to come quickly. A bright sun was overhead, shining over the war-torn planet. Destruction was rampant, yet still the humans and reploids tried to co-exist and rebuild. There were no longer any "Maverick" threats during the previous night after the one Mega Man X dealt with. It was even suspected that those might just be rogue reploids that hadn't gotten it out of their heads that the war was over.

For the first time in a while, X found himself to be bored. The day brought nothing. He inspected some factories for a few hours, and all seemed well. Everyone, despite all that had happened in the past years, still seemed dedicated to repairing the planet. When night hit again he decided to practice his skills in the simulator. That was the least he could do to stay sharp. Instructing the computer to start out with easy stuff and then to move up some of the recorded "Maverick bosses" he had defeated in the past.

X made short work of the enemies that came. The room became covered in plasma fire as various robots tried to kill him. All were unsuccessful. He jumped, dashed, jumped off walls, rolled. . . . Nothing could hit him. He reserved a shot for each guy. It reminded him of his past battles, except it wasn't real. He wasn't killing anyone. With his confidence level rising, he made a quick pose and blasted the last enemy. Time for a Maverick Boss!

But suddenly things began to change. An all-too-familiar form appeared right before his eyes. In a way he wasn't surprised: Vile! It was Vile in his original form to be precise, the one when they first encountered. Vile was quick to fire the disable shot from his shoulder cannon. X had actually been caught off-guard by this sudden change of "bosses," and couldn't quite react quickly enough. Somehow, the shot felt just like how it had in the old days. But why?!

Anger filled him and he exploded out of the force field. Vile was surprised. X had a fully charged straight for him. One well-aimed shot and it hit Vile right in the chest, knocking him to his back. Then, the room cleared back to its normal form. Surprised, X looked around wildly.

"Ha! Caught you off guard there, eh X?" came Zero's laughing voice over the intercom. "You really should really quit wasting your time with nobodies and fight _real_ enemies like your old pal Vile!" His laughing continued.

X calmed down immediately. _Always with the jokes, Zero_, he thought to himself. Mega Man X couldn't help but to smile, and he left the simulator satisfied with this training. However, he was still bothered by Vile's once again strange appearance. Was it mere coincidence? X shrugged it off and decided he would take it easy for the night.


	4. Chapter 3

_Zombie here. Hope you folks like the story so far. I wanted to get this chapter out sooner, but there were delays due to my schedule. I'm sure you know how that goes. By the way, feel free to tell me what you think with reviews if you want! They are most appreciated! Anyways, on to the fic. . . ._

* * *

**Chapter III**

Several days passed without any serious problem. The flashbacks continued to return, but not quite as bad as they were. X figured it was just perhaps some form of battle fatigue, and he decided maybe he did need a break. The problems were indeed minor. . . A few rogue reploids here and there and the problem was done with. He let the lower class Hunters deal with it, and sometimes even just the local police were able to deal with the problems. X continued on with his daily routines, despite what seemed like the constant reappearance of his old rival Vile.

Sure, he saw Sigma and a lot of the other enemies, but it was Vile's image that seemed to constantly come up more then any other. Finally he decided to ask Zero about Vile, who had known Vile before X.

"What did you think of him?" X asked him casually.

Zero thought about it for a moment and then said, "I specifically remember him as being _crazy_. He was a top notch Hunter formerly, but I heard that even in those days he was crazy. The bastard took his job quite seriously! Taking out an entire building filled with innocent people to eliminate a single Maverick!"

X nodded. "Yeah, Vile was crazy. I guess I just look back on him because he was my first real threat."

Zero grinned. "You worry too much about those kinds of things, X. I say the direction is forward!"

X couldn't help but to smile. "That's right! Well I'm outta here Zero!"

Zero did a kind of salute with his hand to wave him off. "Yeah, X."

Mega Man X left, but Zero's words did little to change how he felt, despite what he himself had said. Hell yeah he was crazy. The guy had wiped out his own factory to destroy him! His insane laughter always seemed to fill his head when he started to seriously look back on Vile. Why couldn't Vile just die and leave him alone?

The planet had suffered greatly from Sigma's mad plans, but it hadn't been the first time. If there was one thing about this planet's inhabitants, it's the persistence of its people, whether it is human or reploid. Construction programs were launched planet-wide to rebuild the war-torn cities. Once again human and reploid worked together on a massive scale. At first there was no trouble, as the few problems that did occur were dealt with quickly and efficiently. However, there always seemed to be some kind of bigger problem out there.

A project to rebuild a destroyed tower about ten miles from the Maverick Hunter HQ was going along smoothly until a number of accidents began to occur. Reploids working on the project were sometimes smashed with huge crates filled with heavy equipment due to poor driving and control of the crane vehicles. Who were driving these vehicles? Humans of course.

The reploids always seemed to get stuck with the difficult work. They were the ones that were risking their lives the taller the tower got. It was estimated this giant building would stand well over 100 stories. That was a long fall. Indeed, it wasn't long until these casualties began to occur. Despite this, the construction continued. The process of rebuilding the Earth's cities was on a very strict deadline. However, one reploid stood above the rest of them. Although still answering to the humans, he was declared the "Project Supervisor." He lived up to this quite well, and he carried out the orders of the people to the fullest. Sitting in his office, he could hear it now:

"Oh, three reploids crushed this week? We'll need replacements! Take care of it immediately!"

And that's what he did. Unfortunately, he didn't have a complete disregard for his own kind like these humans did. At first he tried to do what he was supposed to do and hope the Tower would be completed as soon as possible. He kept things on schedule, something they liked. Despite the losses the project continued, and he soon became tired of it. His workers respected him and followed his orders. It was through him that the humans controlled. As the days went by and the project neared its end, his mind had already been taken by the Virus. Hatred flowed through him and his workers were quick to join him.

The Project Supervisor was no pushover. Standing at eight feet tall and had enough strength to lift boulders weighing in the tons. He looked like a reploid construction worker with the yellow hat and square chin. They had built him to be strong enough to work on such large projects as these. The Supervisor was clever, and he quickly saw the human's weaknesses and how useless they had truly become. Turning their construction vehicles of war with modified armor and added armory. Anything could be bought, and what better way to use project funds then to order weapons? The main weapon was the large crane, as it was fitting with blaster turrets and the crane shortened to provide for faster crushing power. It was a perfect killing machine, as it was also large enough to hold not only the Supervisor himself, but also six of his worker-turned-soldier followers.

Three days before the initial completion of their vehicles, they had rounded up all the human workers. Keeping a low profile, they continued to work on the tower project while at the same time the reploids constructed what were basically construction vehicles turned into tanks. And when they attacked the whole city knew it.

Up to then it had been uneventful. Zero had led a few of the newer Maverick Hunters on a simulation raid. Two of them were killed and Zero killed each and every one of the enemies himself .Overall the simulation was a success. Other then that the day was boring. He merely roamed around the headquarters, not really having anything planned. X was out and about as always. He spent hours in the simulators lately, but that was alright he supposed. X was a dedicated fighter, but so was Zero!!

Still, Zero honestly didn't really feel like doing anything right now. When he walked into the command center it was mainly to annoy the operators. Instead, the siren went off.

"Zero!" one of the operators shouted loudly. "The city is under attack! Looks like some reploids have gone Maverick!"

"Maverick huh? There hasn't been an attack in a while, so maybe the Virus is starting to disappear."

Nobody was surprised when X showed up almost immediately.

"Sir, there appears to be four large vehicles destroying everything in their paths. Looks like they originated from the Tower construction site!"

"What?!" X exclaimed. The threat actually sounded as if it might have some kind of significance for once. "How armed are they?"

"We're not entirely sure, but reports on the ground indicate that their armed to the maximum!"

"Sounds fun," Zero said confidently. "Looks like one of the vehicles is more powerful then the other two. X, you take care of that and another while I take care of the other two!"

X nodded. "Right!"

They dashed out of the command center with quick speed and were on their way. Little did they know that this threat was actually well-planned. These reploids had a mission, and that was to further their cause across the city.

* * *

_Author Note: I hate to end the chapter there, but I wanted to get a chapter out to show everybody that I am trying to get this one written. The next chapter will be action-packed!!_


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